Newborn had no problem with BM. Now he is 3 months old and can only go if helped with a thermometer. Any help?

Have tried pear and prune juice. Is currently feed and occasionally supplemented with formula since feeding every 2 hours all night long. BM difficulty does not seem to change based on feed vs. formula. Doctor says he will grow out of it/ wait up to a week and let him go on his own. He was examined and does not have a physical problem with his rectum.